Differential expression of SlKLUH controlling fruit and seed weight is associated with changes in lipid metabolism and photosynthesis related genes.

The size of plant organs such as fruit and seed are crucial yield components. Tomato KLUH underlies the QTL fw3.2 that is an important regulator of fruit and seed weight. However, the mechanism by which the expression levels of KLUH affects organ size is poorly understood. Here, we found that higher expression of SlKLUH increased cell proliferation in the pericarp within five days post anthesis (DPA) in tomato near-isogenic lines (NILs). Differential gene expression analyses showed that lower expression of SlKLUH was associated with increased expression of genes involved in lipid metabolism, especially genes involved in 'Cutin synthesis and transport' and 'Fatty acid elongation and wax biosynthesis'. Lipidomic analysis revealed that repression of SlKLUH mainly increased the contents of certain non-phosphorus glycerolipids and phospholipids and decreased four unknown lipids contents. Over-expression of a transcription factor that is known to influence lipids biosynthesis, SlSHN1, resulted in decreased fruit and seed weight, which supported the notion that changes in lipid metabolism may control organ size. Furthermore, co-expression network analyses revealed that lipid metabolism was possibly associated but not directly regulated by SlKLUH, and that this gene instead was regulating photosynthesis-related processes. In addition, many transcription factors (TFs) putatively involved in KLUH pathway were identified. Collectively, we show that SlKLUH regulates fruit and seed weight that is associated with altered lipid metabolism. The results from this study not only expand our understanding of fruit and seed weight regulation but also offer a valuable resource for functional studies of candidate genes putatively involved in the regulation of organ size in tomato and other crops.